For now the information you are getting is incorrect and Pwnage Tool 3.1.3 will not work on a 3GS with 3.1 factory installed (3.1 out of the box).

Here is a copy and paste straight from the Dev-Team's blog:

"The iPhone 3GS is now supported in PwnageTool 3.1.3, assuming the phone was pwned at 3.0 or 3.0.1 - PwnageTool does not support the 3GS out of the box. If your iPhone 3GS has 3.1 preinstalled and is not Pwned then there is no tested jailbreak solution at the moment."